He began to organize the International Jewish Anti-Fascist Committee.[1] During this time he established contacts with Stanisław Kot, the Polish ambassador in Moscow, and called for Polish Jews in the Soviet Union to join the Polish Anders Army.[2] In October 1941, Alter, together with Henrik Erlich were placed by the Soviet authorities in a hotel in Kuibishev (Samar). During private conversations, which were taped and reported to Joseph Stalin, the two discussed the rumors about the murder of Polish officers, including many Polish Jews, at Katyn.[2] On 4 December 1941, he was again arrested by the NKVD, together with Erlich[2] and murdered, although the precise details about his death are unknown.[1] According to some reports, he was sentenced to death on 23 December 1941, and immediately executed. Other sources state that his execution did not take place until February 1943. The death sentence was signed by Vyacheslav Molotov in a note to Lavrentiy Beria, stating that Stalin had personally approved the order.[3]

In 1943, Soviet authorities issued a communique which announced that Victor Alter had been executed for “spying for Hitler”. His execution, on Stalin's orders,[4] provoked an international outcry.[1]

On February 8, 1991, Victor Erlich, the grandson of Henryk Erlich was informed that according to a decree passed under Russian presidentBoris Yeltsin, Victor Alter, together with Erlich had been "rehabilitated" and the repressions against them had been declared unlawful.[3]

While the exact place where he was buried is unknown, a symbolic monument was erected at the Jewish cemetery on Okopowa street in Warsaw on April 17, 1988. The inscription reads "Leaders of the Bund, Henryk Erlich, b. 1882, and Wiktor Alter, b. 1890. Executed in the Soviet Union". The establishment of the monument (as well as the publication of the full story of Alter and Erlich) was opposed by Poland's post-war communist government and was only made possible due to the efforts of Marek Edelman (sole surviving participant of the Warsaw Ghetto Uprising and a Bundist) and members of the Polish Solidarity Union.[3] The commemoration ceremony was attended by over three thousand people.[3]